PDB-7z0n: Structure-Based Design of a Novel Class of Autotaxin Inhibitors B...

ID or keywords:

Entry

Database: PDB / ID: 7z0n

Title

Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators

Components

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

Keywords

HYDROLASE /

Autotaxin /

ENPP2 /

lysophosphatidic acid /

steroid /

cancer /

fibrosis

Function / homology

Function and homology information

response to polycyclic arene /

alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process /

lysophospholipase activity / positive regulation of lamellipodium morphogenesis /

phosphodiesterase I activity / scavenger receptor activity /

alkylglycerophosphoethanolamine phosphodiesterase activity ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Salgado-Polo, F. / Clark, J.M. / Macdonald, S.J.F. / Barrett, T.N. / Perrakis, A. / Jamieson, A.

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators.
Authors: Clark, J.M. / Salgado-Polo, F. / Macdonald, S.J.F. / Barrett, T.N. / Perrakis, A. / Jamieson, C.

History

Deposition	Feb 23, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 11, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7z0n.cif.gz	608.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7z0n.ent.gz		Display	PDB format
PDBx/mmJSON format	7z0n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z0/7z0n ftp://data.pdbj.org/pub/pdb/validation_reports/z0/7z0n	HTTPS FTP

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Related structure data

Related structure data	5xr9S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #74 - Feb 2006 alpha-Amylase similarity (1) #83 - Nov 2006 Fibrin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

AAA: Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

hetero molecules

96.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	62.788, 89.607, 77.550
Angle α, β, γ (deg.)	90.000, 102.908, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 1 molecules AAA

#1: Protein	Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 / E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD Mass: 92576.094 Da / Num. of mol.: 1 / Mutation: N53A N410A N806A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Plasmid: pcDNA5.1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase

#1: Protein

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 / E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD

Mass: 92576.094 Da / Num. of mol.: 1 / Mutation: N53A N410A N806A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Plasmid: pcDNA5.1 / Cell line (production host): HEK293T / Production host:

Homo sapiens (human)
References: UniProt: Q64610,

alkylglycerophosphoethanolamine phosphodiesterase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide

alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...

Type: oligosaccharide

/ Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-g1_e2-f1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}	LINUCS	PDB-CARE

#3: Sugar

ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose /

Mannose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

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Non-polymers , 8 types, 293 molecules

#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#7: Chemical	ChemComp-SCN / THIOCYANATE ION / Thiocyanate Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#8: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#10: Chemical	ChemComp-I8K / [4-[1-[(4~{R})-4-[(3~{R},5~{S},7~{S},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7-bis(oxidanyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoyl]piperidin-4-yl]oxyphenyl]-bis(oxidanyl)-$l^{4}-borane Mass: 596.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₅H₅₅BNO₆ / Feature type: SUBJECT OF INVESTIGATION
#11: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: ATX was incubated with each screened compound at a 1:10 (protein:compound) ratio for at least 30 minutes. Crystals were grown for at least 7 days in a 24-well optimization screen: 18 to 20% ...Details: ATX was incubated with each screened compound at a 1:10 (protein:compound) ratio for at least 30 minutes. Crystals were grown for at least 7 days in a 24-well optimization screen: 18 to 20% PEG 3350, 0.1 to 0.4 M NaSCN, and 0.1 to 0.4 M NH4I.

Crystal

Density Matthews: 2.34 Å³/Da / Density % sol: 47.37 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: ATX was incubated with each screened compound at a 1:10 (protein:compound) ratio for at least 30 minutes. Crystals were grown for at least 7 days in a 24-well optimization screen: 18 to 20% ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 0.999995 Å

Detector

Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 5, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.999995 Å / Relative weight: 1

Reflection

Resolution: 2.4→46.13 Å / Num. obs: 32870 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC_1/2: 0.982 / R_merge(I) obs: 0.099 / R_pim(I) all: 0.093 / R_rim(I) all: 0.136 / Net I/av σ(I): 7.8 / Net I/σ(I): 7.8

Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
8.98-46.13	0.041	22.2	651	0.978	0.04	0.057	99.3
2.4-2.49	0.621	1.7	3460	0.76	0.576	0.849	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
Aimless		data scaling
Coot		model building
MolProbity		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5XR9

5xr9

Resolution: 2.4→46.13 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.901 / SU B: 26.939 / SU ML: 0.293 / Cross valid method: FREE R-VALUE / ESU R: 0.657 / ESU R Free: 0.301
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.263	1631	4.965 %
R_work	0.1978	31221	-
all	0.201	-	-
obs	-	32852	99.933 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 45.694 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.47 Å²	0 Å²	0.565 Å²
2-	-	3.491 Å²	0 Å²
3-	-	-	-1.158 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→46.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6381	0	194	271	6846

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	6805
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.015	6141
X-RAY DIFFRACTION	r_angle_refined_deg	1.484	1.675	9216
X-RAY DIFFRACTION	r_angle_other_deg	1.227	1.597	14239
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.247	5	796
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.532	21.518	369
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.258	15	1102
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.435	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	870
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7487
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1572
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1471
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	6109
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	3209
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	2966
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	305
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.226	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.237	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.234	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.19	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	1.716	2.387	3184
X-RAY DIFFRACTION	r_mcbond_other	1.707	2.382	3177
X-RAY DIFFRACTION	r_mcangle_it	2.611	3.572	3970
X-RAY DIFFRACTION	r_mcangle_other	2.611	3.572	3970
X-RAY DIFFRACTION	r_scbond_it	1.806	2.554	3621
X-RAY DIFFRACTION	r_scbond_other	1.806	2.554	3621
X-RAY DIFFRACTION	r_scangle_it	2.744	3.762	5244
X-RAY DIFFRACTION	r_scangle_other	2.744	3.762	5244
X-RAY DIFFRACTION	r_lrange_it	4.806	28.552	7585
X-RAY DIFFRACTION	r_lrange_other	4.789	28.443	7561

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4-2.462	0.388	108	0.283	2305	X-RAY DIFFRACTION	100
2.462-2.53	0.321	131	0.284	2242	X-RAY DIFFRACTION	99.9579
2.53-2.603	0.31	124	0.258	2172	X-RAY DIFFRACTION	100
2.603-2.683	0.329	104	0.252	2111	X-RAY DIFFRACTION	100
2.683-2.771	0.294	102	0.234	2040	X-RAY DIFFRACTION	100
2.771-2.868	0.259	112	0.229	2007	X-RAY DIFFRACTION	100
2.868-2.976	0.29	105	0.233	1904	X-RAY DIFFRACTION	100
2.976-3.098	0.312	100	0.226	1824	X-RAY DIFFRACTION	99.7925
3.098-3.235	0.245	73	0.213	1795	X-RAY DIFFRACTION	99.8397
3.235-3.393	0.297	82	0.195	1699	X-RAY DIFFRACTION	100
3.393-3.576	0.213	81	0.178	1614	X-RAY DIFFRACTION	100
3.576-3.793	0.244	82	0.174	1514	X-RAY DIFFRACTION	99.75
3.793-4.054	0.278	81	0.175	1442	X-RAY DIFFRACTION	100
4.054-4.378	0.218	74	0.16	1333	X-RAY DIFFRACTION	99.7872
4.378-4.795	0.24	78	0.154	1216	X-RAY DIFFRACTION	100
4.795-5.359	0.234	53	0.152	1113	X-RAY DIFFRACTION	99.8288
5.359-6.184	0.264	49	0.187	1006	X-RAY DIFFRACTION	100
6.184-7.565	0.235	43	0.192	836	X-RAY DIFFRACTION	100
7.565-10.661	0.154	29	0.155	667	X-RAY DIFFRACTION	100
10.661-46.13	0.255	20	0.189	380	X-RAY DIFFRACTION	98.7654

Refinement TLS params.

Method: refined / Origin x: 13.6499 Å / Origin y: -0.124 Å / Origin z: 16.2647 Å

	11	12	13	21	22	23	31	32	33
T	0.0459 Å²	-0.0203 Å²	-0.0244 Å²	-	0.1985 Å²	0.007 Å²	-	-	0.0172 Å²
L	1.3741 °²	-0.1917 °²	0.5692 °²	-	0.8642 °²	-0.4125 °²	-	-	2.1967 °²
S	0.0449 Å °	-0.1133 Å °	-0.0407 Å °	0.0215 Å °	0.0241 Å °	-0.0118 Å °	-0.0395 Å °	-0.0491 Å °	-0.069 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	56 - 860
2	X-RAY DIFFRACTION	1	ALL	AaA	901
3	X-RAY DIFFRACTION	1	ALL	AbA	902
4	X-RAY DIFFRACTION	1	ALL	AcA	903
5	X-RAY DIFFRACTION	1	ALL	AdA	1205
6	X-RAY DIFFRACTION	1	ALL	AeA	1003
7	X-RAY DIFFRACTION	1	ALL	AfA	1005
8	X-RAY DIFFRACTION	1	ALL	AgA	1202
9	X-RAY DIFFRACTION	1	ALL	AhA	1007
10	X-RAY DIFFRACTION	1	ALL	AiA	904
11	X-RAY DIFFRACTION	1	ALL	AjA	905
12	X-RAY DIFFRACTION	1	ALL	AkA	907
13	X-RAY DIFFRACTION	1	ALL	AlA	908
14	X-RAY DIFFRACTION	1	ALL	AmA	909
15	X-RAY DIFFRACTION	1	ALL	AnA	910
16	X-RAY DIFFRACTION	1	ALL	AoA	915
17	X-RAY DIFFRACTION	1	ALL	ApA	918
18	X-RAY DIFFRACTION	1	ALL	AqA	920
19	X-RAY DIFFRACTION	1	ALL	ArA	922
20	X-RAY DIFFRACTION	1	ALL	AsA	925
21	X-RAY DIFFRACTION	1	ALL	AtA	926
22	X-RAY DIFFRACTION	1	ALL	AuA	928
23	X-RAY DIFFRACTION	1	ALL	AvA	929
24	X-RAY DIFFRACTION	1	ALL	AwA	930
25	X-RAY DIFFRACTION	1	ALL	AxA	933
26	X-RAY DIFFRACTION	1	ALL	AyA	935
27	X-RAY DIFFRACTION	1	ALL	AzA	937
28	X-RAY DIFFRACTION	1	ALL	ABA	1001
29	X-RAY DIFFRACTION	1	ALL	ACA	1101
30	X-RAY DIFFRACTION	1	ALL	ADA	1203

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